DOVER — The Environmental Appeals Board has rejected an appeal from the Municipal Coalition of Portsmouth, Dover and Rochester of a Clean Water Permit issued to the Town of Newmarket.

That appeal challenged the science used by the state Department of Environmental Services and the Environmental Protection Agency to issue permits to municipalities effecting the water quality of the Great Bay, which was designated as impaired for nitrogen in 2009.

In September, Dover City Manager Mike Joyal said the Coalition attempted to withdraw its petition, but their request was denied. According to Jeff Barnum, waterkeeper for the Great Bay-Piscataqua region, this was because the appeals board had already conducted the majority their work in reviewing the 2009 Criteria Document, which the coalition contended did not base its conclusions on accurate science.

Joyal has said natural conditions could be more to blame for the conditions in the Great Bay, rather than discharge from wastewater treatment plants.

“We’re not surprised by the decision,” Joyal said. “The communities did, in fact, seek to withdraw. They did not see a need to pursue any further action through the appeals board because we were able to work cooperatively with the NH DES to arrange for an outside, independent review of the science.”

According to Joyal, that peer review is intended to take into account new information that the Coalition provided to the EAB, but was not considered in the appeal process. Joyal said the Coalition will continue its independent review in the hopes of getting the science right and finding a solution to help clean up the Great Bay.

“It’s important that if we’re going to spend a significant amount of public dollars, it’s going to have the desired result,” Joyal said. “We want to do the right thing.”

Joyal said Coalition members absolutely believe in the importance of reducing nitrogen levels, but disagree on what he feels are the EPA’s extreme demands.

In a press release from the Conservation Law Foundation announcing the decision, the CLF said EAB judges dismissed the appeal due to its belief that the science used to conduct the 2009 study was sound.

“This is a critically important decision for cleaning up the Great Bay estuary,” said Tom Irwin, CLF New Hampshire director, in the release. “It’s a vindication of what scientists have been saying about Great Bay for years — that there’s too much nitrogen pollution — and of needed actions to reduce that pollution to protect our waters.”

The Municipal Coalition’s review of the 2009 Criteria Document is expected to be completed by January 2014.